BN1076 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 5 4.3202e-05 1.0331e-03
Layer 3 1.2253e-04 1.8378e-02
Layer 4 1.7610e-04 9.5519e-04
Layer 6 8.2806e-04 3.3705e-03
Layer 2 5.4847e-03 8.7196e-02
WM 6.6380e-03 7.4244e-02
Layer 1 4.8196e-01 4.1890e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 6 2.6133 0.7303
TUBB4B Layer 5 2.4883 0.6815
SYT1 Layer 5 2.3965 0.6665
NDRG4 Layer 4 2.7129 0.6653
CPLX1 Layer 4 2.4844 0.6646
ENO2 Layer 4 2.6836 0.6596
CHCHD10 Layer 5 2.4238 0.6566
STX1A Layer 5 2.2578 0.6555
ATP6V0A1 Layer 4 2.1777 0.6554
SH3GL2 Layer 6 2.4238 0.6535
STMN1 Layer 5 2.3496 0.6530
GPI Layer 5 2.2266 0.6518
SYP Layer 5 2.4395 0.6493
SULT4A1 Layer 5 2.2617 0.6492
SSBP3 Layer 4 2.2871 0.6491
EEF1A2 Layer 6 2.4570 0.6470
CTSD Layer 5 2.6543 0.6458
DYNC1H1 Layer 5 2.1445 0.6452
SPOCK1 Layer 5 2.3438 0.6449
DPYSL2 Layer 5 2.3652 0.6444
CLSTN1 Layer 6 2.3652 0.6429
MTCH1 Layer 6 2.4180 0.6422
ATP5F1B Layer 5 2.5449 0.6397
BMERB1 Layer 5 2.3652 0.6361
TLE5 Layer 5 2.4941 0.6351
ATP1A3 Layer 6 2.4570 0.6343
TTC9B Layer 4 2.4727 0.6321
DNM1 Layer 5 2.3438 0.6303
NGRN Layer 5 2.4238 0.6297
APP Layer 4 2.1973 0.6296
ATP6V1B2 Layer 5 2.5117 0.6268
TUBB2A Layer 5 2.5332 0.6268
SYN1 Layer 4 2.6016 0.6267
STMN2 Layer 5 2.7715 0.6258
MYO5A Layer 4 2.2578 0.6252
AP2M1 Layer 5 2.3242 0.6252
ATP5F1A Layer 5 2.3750 0.6246
TUBB Layer 5 2.4297 0.6244
TAGLN3 Layer 6 2.5605 0.6239
CABP1 Layer 6 2.5059 0.6238
RAB3C Layer 5 2.2578 0.6234
HIGD1A Layer 6 2.1289 0.6232
KIF3C Layer 6 2.1543 0.6229
RTN1 Layer 6 2.2461 0.6219
FKBP8 Layer 6 2.6250 0.6218
NAPB Layer 6 2.6719 0.6198
LDHA Layer 5 2.4785 0.6194
RTN3 Layer 5 2.3555 0.6186
HCFC1R1 Layer 5 2.4297 0.6186
KIF1A Layer 5 2.2676 0.6169

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1076
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1076_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1076/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1076/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1076/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1076/report/PD/BN1076_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1076/report/PD/BN1076_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 02:13:48
  • Number of Processes: 10
  • Spending Time: 0h 2m